2cdq
Crystal structure of Arabidopsis thaliana aspartate kinase complexed with lysine and S- adenosylmethionine
SAXS 散射曲线 SAXS Profile
P(r) 距离分布 P(r) Distribution
1. 结构基本信息 1. Structure Basics
| 条目编号 entry_id | 2cdq |
| 沉积日期 deposition_date | 2006-01-26 |
| 结构标题 title | Crystal structure of Arabidopsis thaliana aspartate kinase complexed with lysine and S- adenosylmethionine |
| 关键词 keywords | ;ASPARTATE KINASE, AMINO ACID METABOLISM, ACT DOMAIN, ALLOSTERY, S-ADENOSYLMETHIONINE, LYSINE, ALLOSTERIC EFFECTOR, PLANT, TRANSFERASE, AMINO ACID BIOSYNTHESIS ;; TRANSFERASE |
| 实验方法 method | X-RAY DIFFRACTION |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 34.47 Å |
| 回转半径 Rg (电子) rg_electron | 34.27 Å |
| 零角强度 I(0) i0 | 158103000.00 |
| 分子量 molecular_weight | 104600.0 kDa |
| 排除体积 excluded_volume | 132660 ų |
| 包络体积 envelope_volume | 166720 ų |
| 水化壳体积 shell_volume | 42224 ų |
| 包络直径 envelope_diameter | 120.7 Å |
| 壳层 Rg shell_rg | 39.36 Å |
| 包络 Rg envelope_rg | 34.25 Å |
| 形状 Rg shape_rg | 34.27 Å |
| 总 Rg total_rg | 34.66 Å |
| 总原子数 total_atoms | 7346 |
| 残基数 n_residues | 940 |
| 球谐函数阶数 n_harmonics | 20 |
| q 范围 q_range | — – 0.5000 Å−1 |
| 数据点数 n_points | 101 |
| 壳层类型 shell_type | directional |
| 溶剂电子密度 solvent_density | 0.3340 e/ų |
| 壳层衬度 contrast_shell | 0.0300 e/ų |
| CRYSOL 版本 crysol_version | 4.1.3 |
3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)
| 最大尺寸 Dmax dmax | 116.8 Å |
| Rg (实空间) rg_real | 34.65 Å |
| Rg 误差 (实空间) rg_real_error | 0.89 Å |
| I(0) (实空间) i0_real | 1.5810e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.4970e+06 |
| Rg (倒空间) rg_reciprocal | 34.54 Å |
| I(0) (倒空间) i0_reciprocal | 158100000.0000 |
| 解质量估计 total_estimate | 0.8500 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 33.0 Å |
| 偏度 Skewness skewness | 0.506 |
| 峰度 Kurtosis kurtosis | -0.322 |
| 角度范围 angular_range | — – 0.2300 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 42530000.0000 |
| 实空间数据点数 n_real_points | 47 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.778; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.768 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 14 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d2cdqa1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.73 — Carbamate kinase-like |
| 超家族 Superfamily superfamily | c.73.1 — Carbamate kinase-like |
| 家族 Family family | c.73.1.3 — PyrH-like |
| 结构域编号 domain_id | d2cdqa2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.18 — ACT-like |
| 家族 Family family | d.58.18.10 — Aspartokinase allosteric domain-like |
| 结构域编号 domain_id | d2cdqa3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.18 — ACT-like |
| 家族 Family family | d.58.18.10 — Aspartokinase allosteric domain-like |
| 结构域编号 domain_id | d2cdqb1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.73 — Carbamate kinase-like |
| 超家族 Superfamily superfamily | c.73.1 — Carbamate kinase-like |
| 家族 Family family | c.73.1.3 — PyrH-like |
| 结构域编号 domain_id | d2cdqb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.18 — ACT-like |
| 家族 Family family | d.58.18.10 — Aspartokinase allosteric domain-like |
| 结构域编号 domain_id | d2cdqb3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.18 — ACT-like |
| 家族 Family family | d.58.18.10 — Aspartokinase allosteric domain-like |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 2cdqA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1160 — Carbamate kinase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acetylglutamate kinase-like |
| 结构域编号 domain_id | 2cdqA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 1320 — Aspartokinase, catalytic domain |
| 结构域编号 domain_id | 2cdqA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 260 — ACT domain |
| 结构域编号 domain_id | 2cdqA04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 260 — ACT domain |
| 结构域编号 domain_id | 2cdqB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1160 — Carbamate kinase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acetylglutamate kinase-like |
| 结构域编号 domain_id | 2cdqB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 1320 — Aspartokinase, catalytic domain |
| 结构域编号 domain_id | 2cdqB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 260 — ACT domain |
| 结构域编号 domain_id | 2cdqB04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 260 — ACT domain |